Stargate Atlantis: Returns
by Atlantisrules
Summary: Taking place after the events of SGA's Finale Enemy at the Gate. Soeone is bend on revenge on the Expedition, while someone else returns, neither are people who the Expedition expected to ever see again...
1. Prologue

Prologue

Twilight, the time between Light and Dark, he thought it was a very appropriate time. The perfect analogy for his work, light with dark, good with bad, all to one purpose. He stood on a balcony on the outer edge of the pier, the city of Atlantis trailing out behind him. He would control it… or destroy it; he had not yet decided which. He smiled, his face made it seem a cruel, harsh thing. Revenge would be his, soon. Very soon…


	2. Chapter 1

Chapter 1

It had been a month since Atlantis had landed near San Francisco after a battle with a ZPM-charged Wraith Hive Ship, a very long, boring month for Ronon.

It seemed everyone had something to do, except for him. John was off, being debriefed by the IOA about his performance over the last several months. Rodney was visiting his sister. Even Woolsey was off the city doing something. Ronon had nothing to do.

Nothing except for Amelia. They had been growing closer over the last month. He would go find her he decided.

Ronon walked into the Control Room, "Amelia!" he called. Amelia turned to him from a station. "Was wondering if you wanted to get some food..."

"I would, but I have to finish this." She replied.

"What is it?" Ronon asked.

"The sensors picked up something passing through the shield last night. Probably a bird, but if I don't have a complete report on it, Woolsey's gonna kill me."

Ronon smiled mischievously, "Woolsey won't be back until tomorrow." He offered her his hand.

She returned the smile, "Right." she took his hand "I guess I can spare time for lunch."

Ronon pulled her up out of her chair, "If you have to look for birds, why do it on an empty stomach?" they walked away together.

***

John was sitting across the table from several IOA representatives, all of them were looking at him except the one looking down at the report, Shen Xiaoyi.

"This next report says that the Human-Wraith Hybrid, you refer to him as Michael, attacked Atlantis." Shen said, "You end your report by stating that Teyla knocked him off of the Central Tower." She looked up at him. "How can you be sure he is dead?"

John raised an eyebrow, surprised at the question. "When is the last time you fell sixty-five stories and survived?" Shen raised an eyebrow at him, "Ma'am", he added.

"It may not be possible for us, but that does not mean it is not for him." she replied.

"The only reason he survived before is because he outsmarted us. There is no way he gout out of this one."

"Your official word on it, is that he is dead?" Shen asked.

"Yes." John replied.

"Very well. Your next report tells about an encounter with the Wraith known as Todd…"

***

The console Amelia had been at beeped. Its search was done. The screen displayed exactly what passed through the shield, but Amelia wasn't there to see it. Chuck moved over to check on the systems. He clicked, thinking about other things and not really paying attention, the screen was deleted, the answer lost. The truth wouldn't be known.


	3. Chapter 2

Chapter 2

Earth, it was a very strange place. He had found an abandoned, ruined building and was set up in the basement. At night he had seen what life was like in this city, so uncivilized, people heading every which way, smiling, almost fake-looking people on screens, telling about recent events in the world.

He had finally formulated his plans. He even had most everything he needed. There was one thing he still needed, a subject.

He headed out into the city, walking down dark; little used streets in the dead of night. There was a small noise, a scraping sound, a boot on the ground. Someone was out there. They were coming towards him. He slipped a small knife out of a sheath strapped to his wrist and held it at the ready.

The man stopped and touched a small object to the side of his head, a gun. "Give me everything you have."

"Are you sure that is wise?" he hissed.

"Are you sure back-talking me is?"

A small smile crossed his face. "Yes." He brought up the knife into the man's stomach, and then ducked. The gun went off as the man fell to the ground. The shot missed his head but cut into his shoulder. He turned down the direction he was heading and ran.

He ran until he reached an intersection with another street, stopped and listened. Nothing but the vehicles, he thought they were called cars, from far off. No one had followed him. He turned to the left and continued to walk, looking for a house with lights still on. There.

He walked up to the house, silently and peered into the window. There were several people sitting watching a screen on the wall. Not this one. There were too many humans. He did not want to attract too much attention by leaving a pile of dead. He walked back to the street and continued down the road.

He turned and started down another street, he saw one house with a light on. He crept up to the window and looked in. A single woman was sitting on a piece of furniture and watching a screen. He smiled, _perfect_.

***

Becky was sitting in front of the TV, half asleep. She spent most of the day training for a marathon and was exhausted. Some blonde news anchor was blabbering on about one thing or another on the TV.

Suddenly a knock came on the door. "Who the hell could that be?" she said aloud as she stood looking at the clock, 10:33.

She opened the door.

***

The woman saw the knife in his hand and opened her mouth to scream. He reacted quickly, grabbing one arm and using it to spin her around, then using the other arm to choke her, cutting off the scream. He held her like that until she collapsed, unconscious.

He waited to make sure she was fully unconscious before picking her up and starting back to his makeshift home.

***

A flash of blue and white light and John was standing in the Control Room next to Woolsey.

"I need a full report on what has happened in my absence." Woolsey began, speaking to the Technicians.

John hurried away before Woolsey found something for him to do. He just wanted to relax after a long couple of days. Maybe he would get lucky and nothing would happen in the next few days. _Its Earth, what really happens here?_

John was not lucky.


	4. Chapter 3

Chapter 3

A smile crept across his face as he walked over to the woman and looked down at her. He thought nothing of her, or the fact that she was about to die. She was just another piece of his plan, a cog in his machine. As she looked up at him in fear a small part of him felt for her, it struggled with the rest of him, wanting not to kill her, wanting to let her live. He simply pushed that away; weakness could not be allowed to interfere. He lifted the syringe that was in his right hand and pressed it into her arm. As the cold liquid entered her bloodstream, the woman screamed.

***

John got exactly what he wanted. A week and nothing happened. He had mainly spent it in his room, reading. It had been almost six years since he started War and Peace, and he wanted to finish it before it became seven. After awhile his mind began to wander, Weir had always encouraged him to go read. Every time she caught him goofing off she would call "Go read John!" with a smile on her face. He missed her, a lot. He thought perhaps there was a… what? A spark? No, that's crazy! But then again… maybe. He shook the thoughts out of his head and tried to focus on the page again.

***

He walked into the room where he had kept the woman. "Good, very good." He said, as he inspected what lay before him. It was time to make himself known. He couldn't wait to see their faces.

***

Just as John finally was able to focus, a voice came over the speakers. "Colonel Sheppard to the Control Room!" John sighed, put the book down and hurried off.

"What's going on?" he asked as he jogged into the Control Room. He noticed a small red dot on the Short Range sensors "What is that?"

"A Dart, flying over San Francisco." Woolsey answered.

"Where the hell did that come from?!" John asked.

McKay spoke up, "From inside the city. We have people moving in on where it came from. That's not the biggest issue."

"What is it?" Woolsey asked.

"It's coming straight towards us" was Rodney's reply.

***

"Shoot it" Ronon said, a bit of an edge in his voice.

"We can't do that." Rodney said.

"Why not?"

"There are a ton of people in San Francisco, someone is going to notice little orange missiles flying out from mid-air and hitting the flying purple thing." Rodney answered, in his usual aggravated voice.

"Jumper." Ronon replied.

"No, same problem " this time from Sheppard.

"So, we're just going to do nothing then?"

Sheppard hesitated before answering, "Pretty much"

"I hate your world, Sheppard." Ronon growled.

"Sir!" Chuck called, "we have an incoming transmission from the dart"

A voice came over the communications console. "Atlantis, I know you are there, respond or I will open fire on the city."

John shared a look with Rodney and Ronon "Is it just me or…"

It came again, "Atlantis, you have thirty seconds or I fire."

John hit the comm. Button "Is this who I think it is?"

A video transmission came in, confirming John's suspicions. "Hello Sheppard."

John glared at him. "Michael. Sorry if I don't seem happy to see you."

Michael laughed. "Well, I am very happy to see you. Good to know I got here before someone else managed to kill you."

"Aren't I lucky?" John muttered.

Woolsey cut in, "what do you want?"

"Ah, Woolsey, isn't it?"

"You obviously want something or else you would not be here." Woolsey stated.

"Let me guess." Sheppard said. "Torren."

"No." Michael said, "I have given up on that line of research. All I want now is the destruction of Atlantis and all on it."

Ronon spoke quietly "Are you sure we can't shoot him down?"

"We can't Ronon." McKay snapped.

Woolsey moved away and spoke into another communications terminal then came back over and spoke quietly to John. "We have two planes coming. Hopefully they will scare him off for now."

"That's all we can do?" John asked.

"The only way to take him out and not have the entire city see it is if he is away from here. People are probably already wondering about the purple "plane" circling a seemingly empty expanse of water." Woolsey replied.

"Right" John said and sighed.

***

The two Air Force Planes streaked over the city and towards the Bay. "This is Black Two. I have a visual on the target."

"Copy, Black Two. Remember, do not fire on it. Chase it off." came the voice of the Technician at Base.

"Will do." Black Two replied.

"Head to the Left, Two. I'll take right."

"Copy, One. Moving Left."

The target noticed them and began to turn.

"He's making a run at us."

"I see it, Two. Hold course."

"Yes sir."

The target twisting and spun at it sped towards them.

"What is that thing?" Black Two muttered. As they got closer, he could see what it was doing. "It's coming right at you, One!"

"I know, moving to evade." Black One replied calmly. He had been in situations like this before; he knew what he was doing. He managed to avoid the target, barely. "Turn about." Both turned to face the target, it was coming back for another run.

"Heading your way again"

"I see it. He's being careful about it this time." One was using that tone of voice, the one that says 'Bring it on, I'm ready and I know I can take you'. The Target was moving more slowly this time. Suddenly a small blue bolt flew out of it and hit Black One, the plane erupted in flames.

"One!" Black Two called out.

"Black Two, what is going on?" the Technician's voice came.

Black Two spoke, shocked, "We just lost Black One."

In his shock, he didn't realize that the target had turned towards him. The last thing he saw was a blue flash, and then flames.

***

McKay looked shocked. "He just took out both of those planes."

"Those were two of this country's highest rated pilots!" Woolsey said incredulously.

John looked grim. "We're going to need a new plan."


End file.
